| Transcription factor binding site orientation and order are major drivers of gene regulatory activity I Georgakopoulos-Soares, C Deng, V Agarwal, CSY Chan, J Zhao, ... Nature communications 14 (1), 2333, 2023 | 43 | 2023 |
| Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina CSY Chan, N Lonfat, R Zhao, AE Davis, L Li, MR Wu, CH Lin, Z Ji, ... Development 147 (14), dev187922, 2020 | 34 | 2020 |
| Functional characterization of Alzheimer’s disease genetic variants in microglia X Yang, J Wen, H Yang, IR Jones, X Zhu, W Liu, B Li, CD Clelland, W Luo, ... Nature genetics 55 (10), 1735-1744, 2023 | 30 | 2023 |
| High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation I Georgakopoulos-Soares, CSY Chan, N Ahituv, M Hemberg Genome biology 23 (1), 159, 2022 | 29 | 2022 |
| Reprogramming sphingolipid glycosylation is required for endosymbiont persistence in Medicago truncatula WM Moore, C Chan, T Ishikawa, EA Rennie, HML Wipf, V Benites, ... Current Biology 31 (11), 2374-2385. e4, 2021 | 18 | 2021 |
| A survey of k-mer methods and applications in bioinformatics C Moeckel, M Mareboina, MA Konnaris, CSY Chan, I Mouratidis, ... Computational and Structural Biotechnology Journal, 2024 | 15 | 2024 |
| Quasi-prime peptides: identification of the shortest peptide sequences unique to a species I Mouratidis, CSY Chan, N Chantzi, GC Tsiatsianis, M Hemberg, N Ahituv, ... NAR Genomics and Bioinformatics 5 (2), lqad039, 2023 | 14 | 2023 |
| Leveraging sequences missing from the human genome to diagnose cancer I Georgakopoulos-Soares, OY Barnea, I Mouratidis, CSY Chan, R Bradley, ... medRxiv, 2021.08. 15.21261805, 2021 | 11 | 2021 |
| Utilizing nullomers in cell-free RNA for early cancer detection A Montgomery, GC Tsiatsianis, I Mouratidis, CSY Chan, M Athanasiou, ... Cancer gene therapy, 1-10, 2024 | 10 | 2024 |
| Peptide absent sequences emerging in human cancers GC Tsiatsianis, CSY Chan, I Mouratidis, N Chantzi, AM Tsiatsiani, NS Yee, ... European Journal of Cancer 196, 113421, 2024 | 7 | 2024 |
| kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species I Mouratidis, FA Baltoumas, N Chantzi, M Patsakis, CSY Chan, ... Computational and Structural Biotechnology Journal 23, 1919-1928, 2024 | 5 | 2024 |
| Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain CH Lin, Y Sun, CSY Chan, MR Wu, L Gu, AE Davis, B Gu, W Zhang, ... Journal of Biological Chemistry 298 (4), 2022 | 5 | 2022 |
| Nucleic quasi-primes: identification of the shortest unique oligonucleotide sequences in a species I Mouratidis, MA Konnaris, N Chantzi, CSY Chan, A Montgomery, ... bioRxiv, 2023.12. 12.571240, 2023 | 4 | 2023 |
| Frequentmers-a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis I Mouratidis, N Chantzi, U Khan, MA Konnaris, CSY Chan, M Mareboina, ... BMC genomics 24 (1), 768, 2023 | 3 | 2023 |
| Cell type- and stage-specific expression of Otx2 is coordinated by a cohort of transcription factors and multiple cis-regulatory modules in the retina C Chan, N Lonfat, R Zhao, A Davis, L Li, MR Wu, CH Lin, Z Ji, CL Cepko, ... BioRxiv, 2019.12. 19.882969, 2019 | 3 | 2019 |
| Integrative single-cell characterization of hypothalamus sex-differential and obesity-associated genes and regulatory elements HP Nguyen, CSY Chan, DL Cintron, R Sheng, L Harshman, M Nobuhara, ... bioRxiv, 2022.11. 06.515311, 2022 | 2 | 2022 |
| Characterization of hairpin loops and cruciforms across 118,065 genomes spanning the tree of life N Chantzi, C Moeckel, CSY Chan, A Nayak, G Wang, I Mouratidis, ... bioRxiv, 2024.09. 29.615628, 2024 | 1 | 2024 |
| Identification of the shortest species-specific oligonucleotide sequences I Mouratidis, MA Konnaris, N Chantzi, CSY Chan, M Patsakis, K Provatas, ... Genome Research, 2025 | | 2025 |
| The topography of nullomer-emerging mutations and their relevance to human disease CSY Chan, I Mouratidis, A Montgomery, GC Tsiatsianis, N Chantzi, ... Computational and Structural Biotechnology Journal 30, 1-11, 2025 | | 2025 |
| Genomic and Transcriptomic Examination of Functional Elements and Absent Sequences CSY Chan UCSF, 2024 | | 2024 |
